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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;</div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma  once</span></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;</div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;cstdint&gt;</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &lt;memory&gt;</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="preprocessor">#include &quot;cudamapper/sketch_element.hpp&quot;</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="preprocessor">#include &quot;cudamapper/types.hpp&quot;</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;</div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespaceclaragenomics.html">claragenomics</a> {</div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;</div><div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1IndexGenerator.html">   26</a></span>&#160;    <span class="keyword">class </span><a class="code" href="classclaragenomics_1_1IndexGenerator.html">IndexGenerator</a> {</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;        <span class="keyword">public</span>:</div><div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;</div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;        <span class="keyword">virtual</span> <span class="keyword">const</span> std::map&lt;representation_t, std::vector&lt;std::unique_ptr&lt;SketchElement&gt;&gt;&gt;&amp; <a class="code" href="classclaragenomics_1_1IndexGenerator.html#afcb587d961a9daa04571c8829f90e1c8">representations_to_sketch_elements</a>() <span class="keyword">const</span> = 0;</div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;</div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;        <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;std::string&gt;&amp; <a class="code" href="classclaragenomics_1_1IndexGenerator.html#afa81976aefc226e0e67bd2dcfa836737">read_id_to_read_name</a>() <span class="keyword">const</span> = 0;</div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;</div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;        <span class="keyword">virtual</span> <span class="keyword">const</span> std::vector&lt;std::uint32_t&gt;&amp; <a class="code" href="classclaragenomics_1_1IndexGenerator.html#adc1c85dbe72a73b6179feb97e80a779a">read_id_to_read_length</a>() <span class="keyword">const</span> = 0;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;</div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;        <span class="keyword">virtual</span> std::uint64_t <a class="code" href="classclaragenomics_1_1IndexGenerator.html#aa86bcec1f034baaaa68e164d1a1d6ac5">number_of_reads</a>() <span class="keyword">const</span> = 0;</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;        <span class="keyword">static</span> std::unique_ptr&lt;IndexGenerator&gt; <a class="code" href="classclaragenomics_1_1IndexGenerator.html#a9eda7c5413587ed1a62d3d32927f4aa2">create_index_generator</a>(<span class="keyword">const</span> std::string &amp;query_filename, std::uint64_t kmer_length, std::uint64_t window_size);</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    };</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;}</div><div class="ttc" id="namespaceclaragenomics_html"><div class="ttname"><a href="namespaceclaragenomics.html">claragenomics</a></div><div class="ttdef"><b>Definition:</b> cudamapper.hpp:17</div></div>
<div class="ttc" id="classclaragenomics_1_1IndexGenerator_html_aa86bcec1f034baaaa68e164d1a1d6ac5"><div class="ttname"><a href="classclaragenomics_1_1IndexGenerator.html#aa86bcec1f034baaaa68e164d1a1d6ac5">claragenomics::IndexGenerator::number_of_reads</a></div><div class="ttdeci">virtual std::uint64_t number_of_reads() const =0</div><div class="ttdoc">returns number of reads </div></div>
<div class="ttc" id="classclaragenomics_1_1IndexGenerator_html"><div class="ttname"><a href="classclaragenomics_1_1IndexGenerator.html">claragenomics::IndexGenerator</a></div><div class="ttdoc">IndexGenerator - generates data structures necessary for building the actualy index. </div><div class="ttdef"><b>Definition:</b> index_generator.hpp:26</div></div>
<div class="ttc" id="classclaragenomics_1_1IndexGenerator_html_adc1c85dbe72a73b6179feb97e80a779a"><div class="ttname"><a href="classclaragenomics_1_1IndexGenerator.html#adc1c85dbe72a73b6179feb97e80a779a">claragenomics::IndexGenerator::read_id_to_read_length</a></div><div class="ttdeci">virtual const std::vector&lt; std::uint32_t &gt; &amp; read_id_to_read_length() const =0</div><div class="ttdoc">returns mapping of internal read id that goes from 0 to number_of_reads-1 to length of the read retur...</div></div>
<div class="ttc" id="classclaragenomics_1_1IndexGenerator_html_afcb587d961a9daa04571c8829f90e1c8"><div class="ttname"><a href="classclaragenomics_1_1IndexGenerator.html#afcb587d961a9daa04571c8829f90e1c8">claragenomics::IndexGenerator::representations_to_sketch_elements</a></div><div class="ttdeci">virtual const std::map&lt; representation_t, std::vector&lt; std::unique_ptr&lt; SketchElement &gt; &gt; &gt; &amp; representations_to_sketch_elements() const =0</div><div class="ttdoc">returns a mapping of sketch element representations to all sketch elements with those representations...</div></div>
<div class="ttc" id="classclaragenomics_1_1IndexGenerator_html_afa81976aefc226e0e67bd2dcfa836737"><div class="ttname"><a href="classclaragenomics_1_1IndexGenerator.html#afa81976aefc226e0e67bd2dcfa836737">claragenomics::IndexGenerator::read_id_to_read_name</a></div><div class="ttdeci">virtual const std::vector&lt; std::string &gt; &amp; read_id_to_read_name() const =0</div><div class="ttdoc">returns mapping of internal read id that goes from 0 to number_of_reads-1 to actual read name from th...</div></div>
<div class="ttc" id="classclaragenomics_1_1IndexGenerator_html_a9eda7c5413587ed1a62d3d32927f4aa2"><div class="ttname"><a href="classclaragenomics_1_1IndexGenerator.html#a9eda7c5413587ed1a62d3d32927f4aa2">claragenomics::IndexGenerator::create_index_generator</a></div><div class="ttdeci">static std::unique_ptr&lt; IndexGenerator &gt; create_index_generator(const std::string &amp;query_filename, std::uint64_t kmer_length, std::uint64_t window_size)</div><div class="ttdoc">create and return an IndexGenerator object </div></div>
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